''cctbx.xfel'' is a suite of software tools designed to process diffraction data from serial femtosecond crystallography (SFX) measurements at an X-ray free-electron laser (XFEL). Built on the Computational Crystallographic Toolbox ([http://cctbx.sourceforge.net ''cctbx'']), the same toolbox on which [http://www.phenix-online.org ''PHENIX''] and [http://adder.lbl.gov/labelit ''LABELIT''] are built, it enables the user to solve difficult problems relating to processing XFEL data. The programs and modules provided by ''cctbx.xfel'' can reduce a large set of still diffraction images recorded at Stanford’s Linac Coherent Light Source ([http://lcls.slac.stanford.edu LCLS]) to a single MTZ file containing merged reflection intensities suitable for structure solution.

''cctbx.xfel'' is a suite of software tools designed to process diffraction data from serial femtosecond crystallography (SFX) measurements at an X-ray free-electron laser (XFEL). Built on the Computational Crystallographic Toolbox ([http://cctbx.sourceforge.net ''cctbx'']), the same toolbox on which [http://www.phenix-online.org ''PHENIX''] and [http://adder.lbl.gov/labelit ''LABELIT''] are built, it enables the user to solve difficult problems relating to processing XFEL data. The programs and modules provided by ''cctbx.xfel'' can reduce a large set of still diffraction images recorded at Stanford’s Linac Coherent Light Source ([http://lcls.slac.stanford.edu LCLS]) to a single MTZ file containing merged reflection intensities suitable for structure solution.

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== [[2014 Tutorials | 2014 Workshop Tutorial: cctbx.xfel ]]==

== ''cctbx.xfel'' resources ==

== ''cctbx.xfel'' resources ==

Revision as of 12:16, 2 August 2014

Open-source tools for free-electron laser data processing

cctbx.xfel is a suite of software tools designed to process diffraction data from serial femtosecond crystallography (SFX) measurements at an X-ray free-electron laser (XFEL). Built on the Computational Crystallographic Toolbox (cctbx), the same toolbox on which PHENIX and LABELIT are built, it enables the user to solve difficult problems relating to processing XFEL data. The programs and modules provided by cctbx.xfel can reduce a large set of still diffraction images recorded at Stanford’s Linac Coherent Light Source (LCLS) to a single MTZ file containing merged reflection intensities suitable for structure solution.

cctbx.xfel resources

The tutorials on this wiki provide detailed instructions for indexing and integrating still diffraction images extracted from the raw data streams recorded at the LCLS, including pre-processing steps such as dark pedestal generation and refinement of the detector geometry of the Cornell–SLAC pixel array detectors (CSPAD) in use at the CXI and XPP end stations. The tutorials also cover tools to efficiently leverage the LCLS computing cluster to process the thousands to millions of diffraction images that can be recorded in a short time.

Overview to the system architecture at LCLS and real-time progress monitoring of data processing

To install cctbx.xfel elsewhere, or to set up an installation for development purposes, see the Installation instructions. For most regular users this should not be necessary; SLAC as well as several other sites already have a generally accessible installation.